Work from the dutchman panel out in all directions. Quarter panel skin where it meets roof slips under. Drill 3 or 4 holes where they meet before you put it on. Spot weld rear window track from your original to the new one after the quarter is on. Prep all areas first where contact weld areas are by sanding off e coat. Weld prime a light coat on those areas. You may or may not need to bend lips that slide over contact areas so that they can go over. Careful!!. Pointed end of pry bar lines up rear valence meeting areas. As you adjust fitting, check everywhere. A smidgen here can change another area big. I used a 3M pad on the inside of the quarter scuffing it, then put shutz on just like the factory did. Before final welding, check meeting gap areas of door and trunk. Adjust trunk and door if nescessary.
I hope you have a good collection of clamps/vice grips of all types and shapes because you're going to be using a lot of them to get everything in place and keep it like that before you do any spot welds.
I will be leading the quarter panel meet areas shortly and will be doing a thread on that. Bondo telegraphs itself noticably and can also crack at that area. I don't care what brand it is. Metal this or that. Body filler should only be used as a skin coat and not a gap filler.